-
Notifications
You must be signed in to change notification settings - Fork 3
/
Copy pathdd-rmarkdown.html
822 lines (624 loc) · 23.9 KB
/
dd-rmarkdown.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
<!DOCTYPE html>
<html lang="" xml:lang="">
<head>
<title>Dynamic Documents using R: Hands-On</title>
<meta charset="utf-8" />
<meta name="author" content="Fernando Hoces de la Guardia, BITSS" />
<meta name="date" content="2023-11-03" />
<script src="libs/header-attrs-2.22/header-attrs.js"></script>
<link href="libs/remark-css-0.0.1/default.css" rel="stylesheet" />
<link href="libs/remark-css-0.0.1/metropolis.css" rel="stylesheet" />
<link href="libs/remark-css-0.0.1/metropolis-fonts.css" rel="stylesheet" />
</head>
<body>
<textarea id="source">
class: center, middle, inverse, title-slide
.title[
# Dynamic Documents using R: Hands-On
]
.subtitle[
## CEGA EASST Fellows Training
]
.author[
### Fernando Hoces de la Guardia, BITSS
]
.date[
### 03 November 2023
]
---
# Before we begin
.font150[
- Clone/download [this repo](https://github.com/BITSS/RT2_remote_2021)
- If you are having issues of bandwith, clone/download [this repo instead]()
]
---
# Dynamic Documents For Computational Reproducibility
.pull-left[
.font140[
- Based on principles of *literate programming* aims at combining code and paper in one single document
- Best framework to achieve the aspirational goal of **one-click reproducible workflow**
- Best two current implementations: `RMarkdown (R)` & `Jupyter (Julia, Python)`. `Stata` is catching up (dyndocs release [here](https://www.stata.com/new-in-stata/markdown/) and reviews [here](http://data.princeton.edu/stata/markdown/markstat.htm) and [here](https://www.bitss.org/2017/09/05/review-of-statas-dyndoc/))
]
]
--
.pull-right[
.font140[
**"Bro-pen" Science Warning Ahead!**
- Dynamic docs are useful, but they are not essential for reproducibility
- They are pack with little quirks that takes a while to master
- Within DD 90% of the values comes from the most basic (default) output. All the other "cool and easy" feature can be not so easy and make you suffer from the "shiny new exit" phenomena
]
]
---
background-image: url("Images/Two universes.png")
background-size: contain
# .font80[Currently code and narrative components live in separate universes ]
---
background-image: url("Images/One universe.png")
background-size: contain
# Dynamic Documents: integrate the two universes!
---
# Dynamic Documents: A Recipe
.font140[
<br>
- 1 simple language that can combine text and code: `Markdown`
- 1 statistical package to do the analysis (`R`, `Python`, `3S's?`)
- 1 machinery to combine analysis and text to create a single output: `Pandoc`
- [Optional-but-not-really] 1 program to bring all the elements together: RStudio/RMarkdown, Jupyter
]
---
background-image: url("Images/RstudioCS.png")
background-size: contain
# Markdown laguange/syntax in 60 seconds
<br><br><br><br><br><br><br><br><br><br><br><br><br>
.right[
[helpful editor](https://stackedit.io/app#)
to get you
started
]
---
background-image: url("Images/RMarkdownFlow.png")
background-size: contain
background-position: 0% 80%
# One Type of Dynamic Document: R Markdown
.font140[
<br>
- `R`: **open source** programming language design for statistical analysis.
- RStudio: free software that provides and Integrated Development Environment (IDE)
- RStudio combines all together: R + Markdown + Pandoc to produce multiple outputs
]
---
background-image: url("Images/RMarkdownOutputFormats.png")
background-size: contain
# R Markdown
---
# Basic Structure
.font150[
<br><br>
- A header
- Text
- Code: inline and chunks
]
---
# Basic Structure: Header
.pull-left[
.font140[
- Controls document-level charchterisitics:
- type of output (.html, .pdf, etc)
- links to other docs (appeareance, bibliography)
- others
- YAML language
- Define by "`---`"
]
]
.pull-right[
.font150[
<br>
```yml
---
title: "Sample Paper"
author: "Fernando Hoces"
output: html_document
---
```
]
]
---
# Basic Structure: Body of Text
.font150[
<br>
```yml
---
header
---
```
This is where you write your paper. Nothing much to add. You can check Markdown [syntax here](https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf). And it can use can type equations using [LaTex syntax](https://www.overleaf.com/learn/latex/Mathematical_expressions)!
]
---
background-image: url("Images/chunk_click.png")
background-position: 90% 30%
background-size: 500px
# Basic Structure: Code Chunks and Inline
.pull-left[
.font130[
```r
---
header
---
```
Body of text.
To begin a piece of code ("code chunk"). Enclose them in the following expression (Ctrl/Cmd + shift/optn + i)
````
```{r, eval=TRUE}
here goes the code
```
````
To write inline use only one Back-tick to open followed by an "r" and one to close.
]
]
---
# Practical Excercise Goals
.font140[
**Primary Goals:**
1. Become familiar with your first DD.
2. Compile an empty (or default) DD into multiple formats.
3. Edit a DD with some narrative, some code (in R) and some math (optional).
4. Present all the results dynamically into multiple outputs.
]
.font140[
**Secondary Goal:**
1. Expose you to some R programming.
2. Entertain you with a fun problem.
]
---
# Hands-on excercise: the birthday problem!
.font140[
<br>
As an illustration lets write a report using the participants in this workshop to illustrate the famous [birthday problem](https://en.wikipedia.org/wiki/Birthday_problem).
>What is the probability that at least two people this room share the same birthday?
>There are 7 in this room.
>Is it something like `\(\frac{7}{365} =\)` 0.019?
]
---
# Create a new RMarkdown File
.font140[
1 - In RStudio: `File-> New File -> RMarkdown...`
2 - Name it, and save it as `/dynamicdocs/first_dd.Rmd`.
3 - Review/edit the header, and delete all the default body of text except for one code chunk.
4 - In that chunk define a seed (`set.seed(1234)`, number of people in the room (`n.pers = ?`), and this other variable:`n.sims = 10000` (will explain later)
5 - Below the first chunk, write down a title (using `#`) and a brief description.
]
---
# The birthday problem: the math
.font140[
Actually the math says otherwise. Define p(n) as the probability that at least one pair has the same birthday, then the `\(1 - p(n)\)` is the probability that all are born in a different day. Which we can compute as:
]
--
.font140[
\begin{align}
1 - p(n) &= 1 \times \left(1-\frac{1}{365}\right) \times \left(1-\frac{2}{365}\right) \times \cdots \times \left(1-\frac{n-1}{365}\right) \nonumber \newline
&= \frac{ 365 \times 364 \times \cdots \times (365-n+1) }{ 365^n } \nonumber \newline
&= \frac{ 365! }{ 365^n (365-n)!} = \frac{n!\cdot\binom{365}{n}}{365^n}\newline
p(n= 7) &= 0.056 \nonumber
\end{align}
]
---
background-image: url("Images/klingon.png")
background-position: 90% 60%
background-size: 200px
count:false
# The birthday problem: the math
.font140[
Actually the math says otherwise. Define p(n) as the probability that at least one pair has the same birthday, then the `\(1 - p(n)\)` is the probability that all are born in a different day. Which we can compute as:
]
.font140[
\begin{align}
1 - p(n) &= 1 \times \left(1-\frac{1}{365}\right) \times \left(1-\frac{2}{365}\right) \times \cdots \times \left(1-\frac{n-1}{365}\right) \nonumber \newline
&= \frac{ 365 \times 364 \times \cdots \times (365-n+1) }{ 365^n } \nonumber \newline
&= \frac{ 365! }{ 365^n (365-n)!} = \frac{n!\cdot\binom{365}{n}}{365^n}\newline
p(n= 7) &= 0.056 \nonumber
\end{align}
]
---
# Code for the math
(`/dynamicdocs/first_dd_solution.Rmd`)
Copy and paste lines below into your `first_dd.Rmd`
.font130[
```latex
\begin{align}
1 - p(n) &= 1 \times \left(1-\frac{1}{365}\right) \times
\left(1-\frac{2}{365}\right) \times \cdots \times
\left(1-\frac{n-1}{365}\right) \nonumber \\
&= \frac{365 \times 364 \times \cdots \times (365-n+1) }{365^n} \nonumber \\
&= \frac{ 365! }{ 365^n (365-n)!} = \frac{n!\cdot\binom{365}{n}}{365^n}\\
\p(n= `r n.pers`) &= `r round(1 - factorial(n.pers) *
choose(365,n.pers)/ 365^n.pers, 3)` \nonumber
\end{align}
```
]
---
count:false
# Code for the math
(`/dynamicdocs/first_dd_solution.Rmd`)
Copy and paste lines below into your `first_dd.Rmd`
.font130[
```latex
\begin{align}
1 - p(n) &= 1 \times \left(1-\frac{1}{365}\right) \times
\left(1-\frac{2}{365}\right) \times \cdots \times
\left(1-\frac{n-1}{365}\right) \nonumber \\
&= \frac{365 \times 364 \times \cdots \times (365-n+1) }{365^n} \nonumber \\
&= \frac{ 365! }{ 365^n (365-n)!} = \frac{n!\cdot\binom{365}{n}}{365^n}\\
*\p(n= `r n.pers`) &= `r round(1 - factorial(n.pers) *
* choose(365,n.pers)/ 365^n.pers, 3)` \nonumber
\end{align}
```
]
---
# Don't like math? Let's run a simple simulation!
.font150[
<br>
1 - Simulate 10^{4} rooms with `\(n = 7\)` random birthdays, and store the results in matrix where each row represents a room.
2 - For each room (row) compute the number of unique birthdays.
3 - Compute the average number of times a room has 7 unique birthdays, across 10^{4} simulations, and report the complement.
]
---
# Code for the simulation
(`/dynamicdocs/first_dd_solution.Rmd`)
.font120[
```r
birthday.prob = function(n.pers_var, n.sims_var) {
# simulate birthdays
birthdays = matrix(round(runif(n = n.pers_var * n.sims_var, min = 1, max = 365) ),
nrow = n.sims_var, ncol = n.pers_var)
# for each room (row) get unique birthdays
unique.birthdays = apply(birthdays, 1,
function(x) length( unique(x) ) )
# Indicator with 1 if all are unique birthdays
all.different = 1 * (unique.birthdays==n.pers_var)
# Compute average time all have different birthdays
result = 1 - mean(all.different)
return(result)
}
bp_sim = birthday.prob(n.pers_var = 21, n.sims_var = 10000)
print(bp_sim)
```
```
## [1] 0.4531
```
]
---
background-image: url("Images/klingon.png")
background-position: 90% 0%
background-size: 200px
count:false
# Code for the simulation
(`/dynamicdocs/first_dd_solution.Rmd`)
.font120[
```r
birthday.prob = function(n.pers_var, n.sims_var) {
# simulate birthdays
birthdays = matrix(round(runif(n = n.pers_var * n.sims_var, min = 1, max = 365) ),
nrow = n.sims_var, ncol = n.pers_var)
# for each room (row) get unique birthdays
unique.birthdays = apply(birthdays, 1,
function(x) length( unique(x) ) )
# Indicator with 1 if all are unique birthdays
all.different = 1 * (unique.birthdays==n.pers_var)
# Compute average time all have different birthdays
result = 1 - mean(all.different)
return(result)
}
bp_sim = birthday.prob(n.pers_var = 21, n.sims_var = 10000)
print(bp_sim)
```
```
## [1] 0.4365
```
]
---
# Results
.font150[
<br>
- Many people originally think of a prob ~ `\(\frac{1}{365} \times n = 0.019\)`
- However the true probability is of `\(p(n= 7) = 0.056\)`
- And the simulated probability is of `\(0.4365\)`
]
<!--
asd <- sapply(1:365, function(x) round(1 - factorial(x) *
+ choose(365,x)/ 365^x, 3) )
plot(1:100, asd[1:100], type = "l")
> asd1 <- function(y) sapply(1:100, function(x) birthday.prob(n.pers_var = x, y) )
> lines(asd1(5), col="red")
> lines(asd1(30), col="blue")
> lines(asd1(100), col="green")
> points(asd1(1000), pch=3)
legend(60, 0.3, legend=c("5 sims", "30 sims", "100 sims", "1000 sims"),
+ col=c("red", "blue", "green", "black"), lty=c(1,1,1,3), cex=0.8)
title(main="main title", sub="sub-title",
xlab="x-axis label", ylab="y-axis label")
-->
---
# Let's try some other outpus
| Output | Additional Step? | Loss | Share | Others |
|-------------|------------------|--------------------------|-----------------------------------------------|---------------------------------------------------------------------------|
| Simple HTML | no | none | one click (RPubs) or <br>"index method" in github | [cheatsheet](https://rmarkdown.rstudio.com/lesson-15.HTML) |
| Word | no | equations, interactivity | attachment | [help](https://ardata-fr.github.io/officeverse/index.html) |
| PDF | no | interactivity | attachment | requires LaTex <br>`install.packages('tinytex')` <br>`tinytex::install_tinytex()` |
| Slides | New File | some diff in syntax | one click / index method | HTML or PDF (with similar <br> characteristics as above) |
| Book | [many](#additional-steps) | - | index method | `install.packages('bookdown')` <br> [book](https://bookdown.org/yihui/bookdown/) |
- Other outputs not covered: Apps (`shiny`), blogs (`blogdown`), packages (`pkgdown`), richer webpages (`pagedown`), and dashboards (`flexdashboard`)
- Explore templates and install `rticles` for more!
---
name: additional-steps
# Additional Steps for Book Output
.font120[
1 - Create a new project: `File-> New Porject... -> New Directory -> Book Project using bookdown`
2 - Place project in independent folder and then convert into a git repo:
`Tools->Project Options`, choose git, then use GitHub app to publish repo.
3 - Place each chapter into a new Rmd, and enumerate them
4 - Go to top-right pane click on `Build -> Build `
5 - (preparation to share) In the file `_bookdown.yml`, add the following lines
-`repo: https://github.com/YOUR-USER-ID/first_book_solution`
-`output_dir: docs`
-`edit: https://github.com/YOUR-USER-ID/first_book_solution/edit/master/%s`
6 - Modify latex engine in code chunk (line 20 of chapter 2) from `latex` to `md`
6 - Build the book again.
7 - To share: push repo into github.com, then go to the repo's URL, then `settings`, `pages`, select `master` branch, select `docs` folder and save
[Here is the repo with the solutions for the book on birthday problem](https://github.com/BITSS/first_book_solution)
]
---
background-image: url("Images/autor_fig.png")
background-position: 50% 50%
background-size: 700px
# Practical Excercise #2: Mostly Harmless Econometrics!
There is a [fantastic Github](https://github.com/vikjam/mostly-harmless-replication) repo that is reproducing results from MHE
Lets use the of examples Figure [5.2.4](https://github.com/vikjam/mostly-harmless-replication/blob/master/05%20Fixed%20Effects%2C%20DD%20and%20Panel%20Data/Figure%205-2-4.r) to show how dynamic docs can be used in data analysis.
---
# Goals for excercise #2
.font140[
**Primary Goals:**
1 - Demonstrate how the **entire workflow** of a study can fit into a DD.
2 - Show how to add options to the header.
3 - Demonstrate how a DD make code readable to non-coders.
**Secondary Goal:**
1 - Expose you to some R programming.
]
---
# Instructions to get started with excercise #2:
.font140[
1 - Create a new blank `.Rmd` file (steps 1 - 3 in from previous ex.)
2 - Save it as `/dynamicdocs/Figure 5-2-4.Rmd`
3 - Look at [this code](https://github.com/vikjam/mostly-harmless-replication/blob/master/05%20Fixed%20Effects%2C%20DD%20and%20Panel%20Data/Figure%205-2-4.r) behind figure 5.2.4.
4 - Start building your own DD to describe what this code does.
We will go step by step using `/dynamicdocs/Figure 5-2-4_solutions.Rmd` as back-up.
]
---
# Description
.font140[
- Begin a new section (`##`), titled "Description"
- Write a brief description of our goal in the DD.
- You might want to insert a reference to the paper: [link here](http://economics.mit.edu/files/589).
- Specific content not so relevant, just refer to "a treatment" and "a outcome".
]
---
# Getting the raw data
.font140[
- Begin a new section (`##`), titled "Raw Data".
- Describe what you will do.
- Create two code chunks:
````
```{r download data, eval=FALSE, echo=TRUE,
warning=FALSE, results='hide', message=FALSE}
here goes the code
```
````
]
---
# Cleaning the data
.font140[
- Begin a new section (`##`), titled "Data Cleaning".
- Describe what you will do:
- Restrict sample to years between 1979 and 1995 (inclusive)
- Guam from the sample (state = 98).
- Create one code chunk:
````
```{r data cleaning, echo=TRUE}
here goes the code
```
````
- Add some description on the data (using dynamic reporting). See solutions (Figure `5-2-4_solutions.Rmd` line 58) for examples.
]
---
# Build the analytic file
.font140[
- Begin a new section (`##`), titled "Build analytic file".
- Describe what you will do.
- We need to construct the following variables:
- Log of total employment
- Normalize the year variable to 1978
- Insert a new code chunk:
````
```{r analytic file, echo=TRUE}
here goes the code
```
````
]
---
# Describe the model to estimate (optional)
.font140[
<br>
- Begin a new section (`##`), titled "Define model to estimate".
- One line describing what we want to estimate (i.e. "We want to estimate a fixed effect model with lead and lag treatment variables").
- A mathematical model that represents the equation to be estimated (look at solutions).
]
---
# Vizualize the results (optional)
.font140[
<br>
- Begin a new section (`##`), titled "Vizualize the results".
- One line describing what we want to estimate (i.e. "This estimates are then used to create figure 3 of the original paper, which is figure 5.2.4 in MHE.").
````
```{r viz}
here goes the code
```
````
]
---
# Practical Excercise #2
.font140[
- Run your version into multiple outputs.
- Run the solutions version into multiple outputs.
- Compare document with original version of the code.
]
---
# Bonus truck: NBER Working Papers!
.font140[
- Remeber the example from yesterday on the half bake analysis of NBER papers in github?
- Fork and clone the repo one more time:
[github.com/fhoces/nber_trends](https://github.com/fhoces/nber_trends)
- Now knit the `.Rmd` file instead.
]
---
# Final Remarks & More Resources
.font140[
- With DD we can get closer to a one-click reproducible workflow.
- Helps to generate 95% of final output, but if you cannot customize your output 100% do the last 5% in the final desired output (word, latex, etc).
- Large amount of great tutorials on the web (check out the [most recent one from RStudio](https://youtu.be/WkF7nqEYF1E)).
- Great examples: blog posts, and [so](https://bookdown.org/ts_robinson1994/10_fundamental_theorems_for_econometrics/vtDma6bZJ/), [many](https://admindatahandbook.mit.edu/book/v1.0/index.html), [books](https://bitss.github.io/ACRE/) (not many papers!).
- Want to learn more: [great free books](https://bookdown.org/) (can you guess how they were written?)
]
</textarea>
<style data-target="print-only">@media screen {.remark-slide-container{display:block;}.remark-slide-scaler{box-shadow:none;}}</style>
<script src="https://remarkjs.com/downloads/remark-latest.min.js"></script>
<script>var slideshow = remark.create({
"ratio": "16:9",
"highlightStyle": "github",
"highlightLines": true,
"countIncrementalSlides": false
});
if (window.HTMLWidgets) slideshow.on('afterShowSlide', function (slide) {
window.dispatchEvent(new Event('resize'));
});
(function(d) {
var s = d.createElement("style"), r = d.querySelector(".remark-slide-scaler");
if (!r) return;
s.type = "text/css"; s.innerHTML = "@page {size: " + r.style.width + " " + r.style.height +"; }";
d.head.appendChild(s);
})(document);
(function(d) {
var el = d.getElementsByClassName("remark-slides-area");
if (!el) return;
var slide, slides = slideshow.getSlides(), els = el[0].children;
for (var i = 1; i < slides.length; i++) {
slide = slides[i];
if (slide.properties.continued === "true" || slide.properties.count === "false") {
els[i - 1].className += ' has-continuation';
}
}
var s = d.createElement("style");
s.type = "text/css"; s.innerHTML = "@media print { .has-continuation { display: none; } }";
d.head.appendChild(s);
})(document);
// delete the temporary CSS (for displaying all slides initially) when the user
// starts to view slides
(function() {
var deleted = false;
slideshow.on('beforeShowSlide', function(slide) {
if (deleted) return;
var sheets = document.styleSheets, node;
for (var i = 0; i < sheets.length; i++) {
node = sheets[i].ownerNode;
if (node.dataset["target"] !== "print-only") continue;
node.parentNode.removeChild(node);
}
deleted = true;
});
})();
// add `data-at-shortcutkeys` attribute to <body> to resolve conflicts with JAWS
// screen reader (see PR #262)
(function(d) {
let res = {};
d.querySelectorAll('.remark-help-content table tr').forEach(tr => {
const t = tr.querySelector('td:nth-child(2)').innerText;
tr.querySelectorAll('td:first-child .key').forEach(key => {
const k = key.innerText;
if (/^[a-z]$/.test(k)) res[k] = t; // must be a single letter (key)
});
});
d.body.setAttribute('data-at-shortcutkeys', JSON.stringify(res));
})(document);
(function() {
"use strict"
// Replace <script> tags in slides area to make them executable
var scripts = document.querySelectorAll(
'.remark-slides-area .remark-slide-container script'
);
if (!scripts.length) return;
for (var i = 0; i < scripts.length; i++) {
var s = document.createElement('script');
var code = document.createTextNode(scripts[i].textContent);
s.appendChild(code);
var scriptAttrs = scripts[i].attributes;
for (var j = 0; j < scriptAttrs.length; j++) {
s.setAttribute(scriptAttrs[j].name, scriptAttrs[j].value);
}
scripts[i].parentElement.replaceChild(s, scripts[i]);
}
})();
(function() {
var links = document.getElementsByTagName('a');
for (var i = 0; i < links.length; i++) {
if (/^(https?:)?\/\//.test(links[i].getAttribute('href'))) {
links[i].target = '_blank';
}
}
})();
// adds .remark-code-has-line-highlighted class to <pre> parent elements
// of code chunks containing highlighted lines with class .remark-code-line-highlighted
(function(d) {
const hlines = d.querySelectorAll('.remark-code-line-highlighted');
const preParents = [];
const findPreParent = function(line, p = 0) {
if (p > 1) return null; // traverse up no further than grandparent
const el = line.parentElement;
return el.tagName === "PRE" ? el : findPreParent(el, ++p);
};
for (let line of hlines) {
let pre = findPreParent(line);
if (pre && !preParents.includes(pre)) preParents.push(pre);
}
preParents.forEach(p => p.classList.add("remark-code-has-line-highlighted"));
})(document);</script>
<script>
slideshow._releaseMath = function(el) {
var i, text, code, codes = el.getElementsByTagName('code');
for (i = 0; i < codes.length;) {
code = codes[i];
if (code.parentNode.tagName !== 'PRE' && code.childElementCount === 0) {
text = code.textContent;
if (/^\\\((.|\s)+\\\)$/.test(text) || /^\\\[(.|\s)+\\\]$/.test(text) ||
/^\$\$(.|\s)+\$\$$/.test(text) ||
/^\\begin\{([^}]+)\}(.|\s)+\\end\{[^}]+\}$/.test(text)) {
code.outerHTML = code.innerHTML; // remove <code></code>
continue;
}
}
i++;
}
};
slideshow._releaseMath(document);
</script>
<!-- dynamically load mathjax for compatibility with self-contained -->
<script>
(function () {
var script = document.createElement('script');
script.type = 'text/javascript';
script.src = 'https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-MML-AM_CHTML';
if (location.protocol !== 'file:' && /^https?:/.test(script.src))
script.src = script.src.replace(/^https?:/, '');
document.getElementsByTagName('head')[0].appendChild(script);
})();
</script>
</body>
</html>